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31
MS-DIAL / Re: MS-DIAL beginner
Last post by biswapriya -
Hello,

1. No- cannot use Metlin unless you buy it (expensive!) and use locally- so possible if you spend USD 5K. Use MSDIAL libraries and also, you can add more LC-MS/MS libraries from MoNA (https://mona.fiehnlab.ucdavis.edu/downloads) and GNPS (https://gnps.ucsd.edu/ProteoSAFe/libraries.jsp). For combining libraries, you can use a simple method like https://www.protocols.io/view/steps-for-building-an-open-source-ei-ms-mass-spect-eq2ly33rqgx9/v1 but for your LC-MS/MS use case use ESI-MS or LC-MS or MS/MS libraries only. Add and combine as many as possible and does not matter Pos or Neg mode as they all help and do not mess up with matching.

2. Export "Area" or "Height" and both works fine for me. If normalized(if you ran multiple pooled QCs)  then hit normalize using LOWESS and QC or using internal standards and then export the "normalized data file" from Alignment Results.

3. Not possible. Export everything and then "filter out your validated". What is your definition of validated? If MS/MS matched with library without RT match, then fine too and can be filtered from the final area/ height file export as "MS/MS pos match" and a "cosine/ dot product" similarity score of say >70 or 0.7.

Hope this helps.

Thanks,
Biswa
32
MS-DIAL / Error with uploading experiment file_data processing with SWATH-MS method type
Last post by Zareen S Khan -
Hello Community,

Season's Greetings! Merry Christmas and Happy New Year!

I have started to use MS-DIAL recently. I face the following error message, ''Invalid analyst experiment information'' while trying to upload the experiment file (.txt) with the experiment information of my DIA method. I am trying to upload the following experimental details saved in a notepad.
Experiment       MS Type  Min m/z   Max m/z
0        SCAN      200       380
1        SWATH    200       210
2        SWATH    210       220
3        SWATH    220       230
4        SWATH    230       240
5        SWATH    240       250
6        SWATH    250       260
7        SWATH    260       270
8        SWATH    270       280
9        SWATH    280       290
10       SWATH    290       300
11       SWATH    300       310
12       SWATH    310       320
13       SWATH    320       330
14       SWATH    330       340
15       SWATH    340       350
16       SWATH    350       360
17       SWATH    360       370
18       SWATH    370       380

I am not sure what is going wrong. Is there any body who experienced something similar or can give any insights to resolve this?
I would be very grateful. Thank you in advance!

Happy Holidays!
Zareen
33
MS-DIAL / .NET format version needed to run
Last post by mw_uwchem -
Hi, does anyone know the .NET format needed to run the latest version of MS Dial? It keeps reading the .NET v4.0 and says its incompatible, despite me downloading the latest version.
34
MS-DIAL / MS-DIAL beginner
Last post by ilaria. -
Hello everyone,
I'm just approaching to use MS-DIAL. I would like to ask some questions about it.

1) Is it possible to introduce METLIN library in the MS-DIAL searching? If not, do you recommend to use just the libraries downloadable from MS-DIAL website for the human metabolome?
2) Which file should I export for the metabolites quantification and which table column should I consider as a normalized value to quantify metabolites?
3) Is it possible to export only the validated metabolites after the post-processing analysis to discard the false positives?

Thank you to everyone who will reply  :)
Ilaria
35
MS-DIAL / MS Dial v5 keeps crashing + Mass normalization
Last post by mw_uwchem -
Hi all,

#1 I'm wondering if there is a solution to the newest version of MS Dial (v5) crashing? Soon after I press "Run", the software closes with no warning or error message. Also- I've updated to the newest pre-released version AND tried another user's solution to add msp files for IDs after running the initial search. When I try this, everything works fine but then the program crashes again once the msp files are uploaded. :( Is this an issue with too large of libraries or too many samples?

#2 I've started using v4.9 and am wondering if there is a scalar to normalize by sample mass? I originally was using the newest version's analytical factor column.

Thanks,
Mallory
39
MS-DIAL / Re: MS-DIAL error. Check polarity setting?
Last post by biswapriya -
Hello,

Please share the a) Parameters.text file that you can save after the analysis is concluded.
b) A link to a RAW file loaded onto Google drive or dropbox will also help me troubleshoot the issue.

Thanks,
Biswa
40
MS-DIAL / Re: No support for custom .msp library in the Lipidomics workflow in MSDIAL 4.9...
Last post by biswapriya -
Hello,
Here is a  solution that has worked for me by asking the software to run a metabolomics analysis, and uplading a lipidomics.msp spectral ibrary:

Hello,

Well, the way lipidomics workflow on MSDIAL is built is that "lipidomics spectral DB" is "inbuilt" and one can not upload external or additional libraries for spectral searches.

if you really have your own and very enriched .msp for lipids, then start as "metabolomics" in the  1st window, and then use the lipidomics .msp as reference spectral library for searching.

This should work for you!

Thanks,
Biswa